Nucleic acid polymer chemistry has played a crucial role in many developing technologies in the pharmaceutical, diagnostic, and analytical fields, and more particularly in the subfields of antisense and anti-gene therapeutics, combinatorial chemistry, branched DNA signal amplification, and array-based DNA diagnostics and analysis e.g. Uhlmann and Peyman, Chemical Reviews, 90: 543-584 (1990); Milligan et al, J. Med. Chem. 36: 1923-1937 (1993); Mesmaeker et al, Current Opinion in Structural Biology, 5: 343-355 (1995); Thuong et al, Angew. Chem. Int. Ed. Engl., 32: 666-690 (1993); Brenner et al, Proc. Natl. Acad. Sci., 89: 5381-5383 (1992); Gold et al, Ann. Rev. Biochem., 64: 763-797 (1995); Gallop et al, J. Med. Chem. 37: 1233-1258 (1994); Gordon et al, J. Med. Chem. 37: 1385-1401 (1994); Gryaznov, International application PCT/US94/07557; Urdea et al, U.S. Pat. No. 5,124,246; Southern et al, Genomics, 13: 1008-1017 (1992); McGall et al, U.S. Pat. No. 5,412,087; Fodor et al, U.S. Pat. No. 5,424,186; Pirrung et al, U.S. Pat. No. 5,405,783; and the like.
Much of this chemistry has been directed to improving the binding strength, specificity, and nuclease resistance of natural nucleic acid polymers, such as DNA. Unfortunately, improvements in one property, such as nuclease resistance, often involve trade-offs against other properties, such as binding strength. Examples of such trade-offs abound: peptide nucleic acids (PNAs) display good nuclease resistance and binding strength, but have reduced cellular uptake in test cultures, e.g. Hanvey et al, Science, 258: 1481-1485 (1992); phosphorothioates display good nuclease resistance and solubility, but are typically synthesized as P-chiral mixtures and display several sequence-non-specific biological effects, e.g. Stein et al, Science, 261: 1004-1012 (1993); methylphosphonates display good nuclease resistance and cellular uptake, but are also typically synthesized as P-chiral mixtures and have reduce duplex stability, e.g. Mesmaeker et al (cited above); and so on.
Recently, a new class of oligonucleotide analog has been developed having so-called N3'.fwdarw.P5' phosphoramidate internucleoside linkages which display very favorable binding properties, nuclease resistance, and solubility, Gryaznov and Letsinger, Nucleic Acids Research, 20: 3403-3409 (1992); Chen et al, Nucleic Acids Research, 23: 2661-2668 (1995); Gryaznov et al, Proc. Natl. Acad. Sci., 92: 5798-5802 (1995); and Gryaznov et al, J. Am. Chem. Soc., 116: 3143-3144(1994). Unfortunately, low synthesis yields of these compounds with published protocols has inhibited their commercial application.
The utility of this new class of oligonucleotide analog would be significantly increased if modifications and new synthesis approaches could be found that would improve synthesis yields without a concomitant loss in any other of its other favorable properties outlined above.